If more than 50 genes/sequences are provided as input, then the associated running time can take some time. Therefore it is advisable to provide an email-address in case you are running the Interactive Phylogenetics Module with more than 50 genes. After processing you will be send an email with a link to the created phylogenetic tree.
The selection modi are exclusive: please choose either Gene selection or Species selection.
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ) $local_species = 'acertr' $disabled = '' $selected = ''include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0;
$disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":"";
$selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":"";
$num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0;
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ) $local_species = 'acertr' $disabled = '' $selected = ''
include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ) $local_species = 'ach' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ) $local_species = 'ach' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ) $local_species = 'aar' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ) $local_species = 'aar' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ) $local_species = 'amhyb' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ) $local_species = 'amhyb' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ) $local_species = 'atr' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ) $local_species = 'atr' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ) $local_species = 'aag' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ) $local_species = 'aag' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ) $local_species = 'aox' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ) $local_species = 'aox' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ) $local_species = 'aly' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ) $local_species = 'aly' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ) $local_species = 'ath' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ) $local_species = 'ath' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ) $local_species = 'arhy' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ) $local_species = 'arhy' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ) $local_species = 'ama' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ) $local_species = 'ama' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ) $local_species = 'bvu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ) $local_species = 'bvu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ) $local_species = 'bca' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ) $local_species = 'bca' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ) $local_species = 'bna' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ) $local_species = 'bna' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ) $local_species = 'bol' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ) $local_species = 'bol' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ) $local_species = 'bra' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ) $local_species = 'bra' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ) $local_species = 'camsi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ) $local_species = 'camsi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ) $local_species = 'cansat' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ) $local_species = 'cansat' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ) $local_species = 'cru' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ) $local_species = 'cru' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ) $local_species = 'can' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ) $local_species = 'can' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ) $local_species = 'chi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ) $local_species = 'chi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ) $local_species = 'cpa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ) $local_species = 'cpa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ) $local_species = 'cfa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ) $local_species = 'cfa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ) $local_species = 'cil' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ) $local_species = 'cil' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ) $local_species = 'cde' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ) $local_species = 'cde' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ) $local_species = 'cbr' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ) $local_species = 'cbr' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ) $local_species = 'cre' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ) $local_species = 'cre' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ) $local_species = 'cla' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ) $local_species = 'cla' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ) $local_species = 'ccl' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ) $local_species = 'ccl' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ) $local_species = 'ccan' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ) $local_species = 'ccan' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ) $local_species = 'col' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ) $local_species = 'col' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ) $local_species = 'cav' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ) $local_species = 'cav' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ) $local_species = 'cme' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ) $local_species = 'cme' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ) $local_species = 'csa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ) $local_species = 'csa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ) $local_species = 'dca' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ) $local_species = 'dca' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ) $local_species = 'din' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ) $local_species = 'din' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ) $local_species = 'dzi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ) $local_species = 'dzi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ) $local_species = 'eca' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ) $local_species = 'eca' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ) $local_species = 'egut' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ) $local_species = 'egut' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ) $local_species = 'egr' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ) $local_species = 'egr' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ) $local_species = 'esa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ) $local_species = 'esa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ) $local_species = 'fve' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ) $local_species = 'fve' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ) $local_species = 'fan' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ) $local_species = 'fan' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ) $local_species = 'gma' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ) $local_species = 'gma' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ) $local_species = 'ghi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ) $local_species = 'ghi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ) $local_species = 'gra' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ) $local_species = 'gra' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ) $local_species = 'han' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ) $local_species = 'han' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ) $local_species = 'hma' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ) $local_species = 'hma' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ) $local_species = 'lsa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ) $local_species = 'lsa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ) $local_species = 'lonja' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ) $local_species = 'lonja' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ) $local_species = 'lja' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ) $local_species = 'lja' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ) $local_species = 'lal' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ) $local_species = 'lal' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ) $local_species = 'mbi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ) $local_species = 'mbi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ) $local_species = 'mdo' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ) $local_species = 'mdo' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ) $local_species = 'mes' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ) $local_species = 'mes' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ) $local_species = 'mpo' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ) $local_species = 'mpo' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ) $local_species = 'mtr' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ) $local_species = 'mtr' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ) $local_species = 'mco' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ) $local_species = 'mco' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ) $local_species = 'nta' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ) $local_species = 'nta' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ) $local_species = 'oeu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ) $local_species = 'oeu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ) $local_species = 'osa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ) $local_species = 'osa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ) $local_species = 'pso' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ) $local_species = 'pso' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ) $local_species = 'pax' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ) $local_species = 'pax' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ) $local_species = 'pvu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ) $local_species = 'pvu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ) $local_species = 'ppa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ) $local_species = 'ppa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ) $local_species = 'psa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ) $local_species = 'psa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ) $local_species = 'ptr' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ) $local_species = 'ptr' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $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 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $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 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ) $local_species = 'pgr' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ) $local_species = 'pgr' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ) $local_species = 'qlo' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ) $local_species = 'qlo' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ) $local_species = 'rsi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ) $local_species = 'rsi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ) $local_species = 'rch' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ) $local_species = 'rch' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ) $local_species = 'sbr' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ) $local_species = 'sbr' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ) $local_species = 'sbo' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ) $local_species = 'sbo' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ) $local_species = 'shi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ) $local_species = 'shi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ) $local_species = 'sed' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ) $local_species = 'sed' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ) $local_species = 'smo' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ) $local_species = 'smo' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ) $local_species = 'sun' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ) $local_species = 'sun' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ) $local_species = 'sgi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ) $local_species = 'sgi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ) $local_species = 'sci' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ) $local_species = 'sci' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ) $local_species = 'sly' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ) $local_species = 'sly' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ) $local_species = 'spe' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ) $local_species = 'spe' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ) $local_species = 'stu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ) $local_species = 'stu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ) $local_species = 'sas' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ) $local_species = 'sas' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ) $local_species = 'tha' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ) $local_species = 'tha' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ) $local_species = 'tca' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ) $local_species = 'tca' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ) $local_species = 'tpr' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ) $local_species = 'tpr' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ) $local_species = 'twi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ) $local_species = 'twi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ) $local_species = 'tar' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ) $local_species = 'tar' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ) $local_species = 'ugi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ) $local_species = 'ugi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ) $local_species = 'vma' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ) $local_species = 'vma' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ) $local_species = 'vpl' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ) $local_species = 'vpl' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ) $local_species = 'vmu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ) $local_species = 'vmu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ) $local_species = 'vvi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ) $local_species = 'vvi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $species_info = array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) $local_species = 'zma' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ), 'gf_id' => 'HOM05D001083', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001083' ), 'data_identifier' => 'HOM05D001083', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001083', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '567', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p15960' => 'bna', 'A01p15970' => 'bna', 'A03p55430' => 'bna', 'A03p55440' => 'bna', 'A05p15250' => 'bna', 'A06p32270' => 'bna', 'A06p39250' => 'bna', 'A10p27100' => 'bna', 'Aa31LG1G16570' => 'aar', 'Aa31LG4G9690' => 'aar', 'Aa31LG4G9700' => 'aar', 'Aa31sc687G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.494' => 'aag', 'Actinidia03356' => 'ach', 'Actinidia06525' => 'ach', 'Actinidia06526' => 'ach', 'Actinidia10373' => 'ach', 'Actinidia10374' => 'ach', 'Actinidia12340' => 'ach', 'Actinidia20613' => 'ach', 'Actinidia29614' => 'ach', 'Actinidia30816' => 'ach', 'Actinidia30817' => 'ach', 'Actinidia30830' => 'ach', 'Ah.01g003430' => 'amhyb', 'Ah.02g125890' => 'amhyb', 'Ah.05g170690' => 'amhyb', 'Ah.05g170700' => 'amhyb', 'Ah.10g024980' => 'amhyb', 'Ah.16g104380' => 'amhyb', 'AL6G20960' => 'aly', 'AL7G28580' => 'aly', 'AL7G28590' => 'aly', 'AL8G21040' => 'aly', 'AL8G43010' => 'aly', 'Aqoxy4G02282' => 'aox', 'Aqoxy5G01324' => 'aox', 'Aqoxy5G01325' => 'aox', 'Aqoxy6G01457' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17KMWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4HU4LR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0ACWS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BPHJ2T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1F113' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP1NWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC25VJ' => 'arhy', 'AT4G24610' => 'ath', 'AT4G24620' => 'ath', 'AT5G48310' => 'ath', 'AT5G65440' => 'ath', 'ATR0022G025' => 'atr', 'ATR0022G035' => 'atr', 'ATR0022G064' => 'atr', 'ATR0751G218' => 'atr', 'Atru.chr13.1039' => 'acertr', 'Atru.chr13.1040' => 'acertr', 'Atru.chr3.1292' => 'acertr', 'Atru.chr5.2857' => 'acertr', 'Atru.chr6.3454' => 'acertr', 'Atru.chr6.3457' => 'acertr', 'Atru.chr6.3458' => 'acertr', 'AUR62003288' => 'cqu', 'AUR62019023' => 'cqu', 'AUR62019024' => 'cqu', 'AUR62025101' => 'cqu', 'AUR62027177' => 'cqu', 'AUR62027860' => 'cqu', 'AUR62027861' => 'cqu', 'AUR62037156' => 'cqu', 'BcaB01g00911' => 'bca', 'BcaB08g37103' => 'bca', 'BcaC01g02763' => 'bca', 'BcaC02g11102' => 'bca', 'BcaC06g30807' => 'bca', 'BcaC06g30810' => 'bca', 'BcaC06g32870' => 'bca', 'BcaC06g32871' => 'bca', 'BcaC06g32872' => 'bca', 'BcaC09g50847' => 'bca', 'BcaC09g50848' => 'bca', 'BcaNung04959' => 'bca', 'BcaNung04960' => 'bca', 'BolC1t01922H' => 'bol', 'BolC1t01923H' => 'bol', 'BolC3t18319H' => 'bol', 'BolC4t23569H' => 'bol', 'BolC7t44427H' => 'bol', 'BolC7t45863H' => 'bol', 'BolC7t45864H' => 'bol', 'BolC8t48580H' => 'bol', 'BolC9t59460H' => 'bol', 'BraA01t01530Z' => 'bra', 'BraA01t01531Z' => 'bra', 'BraA03t14617Z' => 'bra', 'BraA03t14618Z' => 'bra', 'BraA05t20444Z' => 'bra', 'BraA06t26153Z' => 'bra', 'BraA06t26839Z' => 'bra', 'BraA10t44762Z' => 'bra', 'C01p19940' => 'bna', 'C01p19950' => 'bna', 'C03p60640' => 'bna', 'C04p20400' => 'bna', 'C04p20410' => 'bna', 'C05p47580' => 'bna', 'C07p39090' => 'bna', 'C07p53720' => 'bna', 'C07p53730' => 'bna', 'C09p66800' => 'bna', 'CAN.G105.25' => 'can', 'CAN.G1375.13' => 'can', 'CAN.G1375.8' => 'can', 'CAN.G1388.10' => 'can', 'CAN.G175.14' => 'can', 'CAN.G585.7' => 'can', 'CAN.G79.68' => 'can', 'CANSAT01G1153' => 'cansat', 'CANSAT25G1784' => 'cansat', 'CANSAT25G2442' => 'cansat', 'CANSAT64G2565' => 'cansat', 'CANSAT80G2842' => 'cansat', 'CARHR183980' => 'chi', 'CARHR232000' => 'chi', 'CARHR232010' => 'chi', 'CARHR279420' => 'chi', 'Carub.0006s0893' => 'cru', 'Carub.0007s1644' => 'cru', 'Carub.0007s1645' => 'cru', 'Carub.0008s0786' => 'cru', 'Carub.0008s2629' => 'cru', 'Ca_05403_v3' => 'car', 'Ca_05404_v3' => 'car', 'Ca_06486_v3' => 'car', 'CBR_g39880' => 'cbr', 'Cc05_g03780' => 'ccan', 'Cc05_g09900' => 'ccan', 'Cc07_g14270' => 'ccan', 'Cc10_g15670' => 'ccan', 'Cc10_g15680' => 'ccan', 'CDE03G0347' => 'cde', 'CDE03G0369' => 'cde', 'CDE06G0642' => 'cde', 'CDE06G1229' => 'cde', 'CDE10G0373' => 'cde', 'CDE10G0693' => 'cde', 'CDE10G0780' => 'cde', 'CDE10G0945' => 'cde', 'CDE10G1263' => 'cde', 'Cfa004353' => 'cfa', 'Cfa010891' => 'cfa', 'Cfa013696' => 'cfa', 'Cfa014188' => 'cfa', 'Ciclev10000059m.g' => 'ccl', 'Ciclev10000603m.g' => 'ccl', 'Ciclev10014121m.g' => 'ccl', 'Ciclev10024732m.g' => 'ccl', 'CiPaw.03G284800' => 'cil', 'CiPaw.07G167400' => 'cil', 'CiPaw.07G167500' => 'cil', 'CiPaw.08G054500' => 'cil', 'ClCG01G018460' => 'cla', 'ClCG02G010600' => 'cla', 'ClCG08G011800' => 'cla', 'ClCG11G014490' => 'cla', 'COL.COLO4_15810' => 'col', 'COL.COLO4_19707' => 'col', 'COL.COLO4_27342' => 'col', 'Cpa.g.c44204' => 'cpa', 'Cpa.g.c44375' => 'cpa', 'Cpa.g.sc136.83' => 'cpa', 'Cpa.g.sc3051.1' => 'cpa', 'Cpa.g.sc309.2' => 'cpa', 'Cpa.g.sc309.3' => 'cpa', 'Cpa.g.sc4189.1' => 'cpa', 'Cpa.g.sc55.39' => 'cpa', 'Cpa.g.sc55.40' => 'cpa', 'Cpa.g.sc8.1' => 'cpa', 'Cpa.g.sc863.2' => 'cpa', 'Cpa.g.sc863.3' => 'cpa', 'Cre06.g278212' => 'cre', 'CsaV3_2G030420' => 'csa', 'CsaV3_3G047900' => 'csa', 'CsaV3_6G009810' => 'csa', 'CsaV3_6G045110' => 'csa', 'CSS0001719' => 'camsi', 'CSS0007953' => 'camsi', 'CSS0020165' => 'camsi', 'CSS0030266' => 'camsi', 'CSS0030378' => 'camsi', 'CSS0034477' => 'camsi', 'CSS0039479' => 'camsi', 'CSS0041566' => 'camsi', 'CSS0042788' => 'camsi', 'CSS0045493' => 'camsi', 'CSS0045832' => 'camsi', 'DCAR_009571' => 'dca', 'DCAR_015973' => 'dca', 'DCAR_019306' => 'dca', 'DCAR_019651' => 'dca', 'Dinv13621' => 'din', 'Dinv20779' => 'din', 'Dinv21335' => 'din', 'Dinv42628' => 'din', 'Dinv42631' => 'din', 'Dinv44842' => 'din', 'Dinv44843' => 'din', 'Duzib041G0389' => 'dzi', 'Duzib041G0775' => 'dzi', 'Duzib093G0227' => 'dzi', 'Duzib116G0753' => 'dzi', 'Duzib138G0365' => 'dzi', 'Duzib264G1317' => 'dzi', 'ECA232G1336' => 'eca', 'ECA232G2539' => 'eca', 'ECA234G4394' => 'eca', 'ECA246G2379' => 'eca', 'ECA246G2462' => 'eca', 'ECA246G4856' => 'eca', 'EL10Ac1g01078' => 'bvu', 'EL10Ac1g01079' => 'bvu', 'EL10Ac6g14786' => 'bvu', 'EL10As4g23423' => 'bvu', 'Eucgr.E02131' => 'egr', 'Eucgr.F00407' => 'egr', 'Eucgr.F02133' => 'egr', 'Eucgr.K01368' => 'egr', 'Eucgr.L02270' => 'egr', 'FAN02G2977' => 'fan', 'FAN04G0690' => 'fan', 'FAN04G2240' => 'fan', 'FAN05G4687' => 'fan', 'FAN08G2447' => 'fan', 'FAN08G3511' => 'fan', 'FAN09G2056' => 'fan', 'FAN13G0758' => 'fan', 'FAN13G1737' => 'fan', 'FAN14G2444' => 'fan', 'FAN18G1491' => 'fan', 'FAN18G4577' => 'fan', 'FAN19G1156' => 'fan', 'FAN23G2438' => 'fan', 'FAN26G1626' => 'fan', 'FAN28G0263' => 'fan', 'FAN28G2556' => 'fan', 'FvH4_1g19880' => 'fve', 'FvH4_5g35670' => 'fve', 'FvH4_5g35680' => 'fve', 'FvH4_6g40180' => 'fve', 'Glyma.01G093600' => 'gma', 'Glyma.02G212600' => 'gma', 'Glyma.02G212700' => 'gma', 'Glyma.02G309200' => 'gma', 'Glyma.04G092400' => 'gma', 'Glyma.06G093000' => 'gma', 'Glyma.06G094300' => 'gma', 'Glyma.14G003600' => 'gma', 'Glyma.14G180501' => 'gma', 'Glyma.14G180600' => 'gma', 'Glyma.19G079850' => 'gma', 'Gohir.A02G077800' => 'ghi', 'Gohir.A05G220800' => 'ghi', 'Gohir.A05G220900' => 'ghi', 'Gohir.A06G032624' => 'ghi', 'Gohir.A07G194400' => 'ghi', 'Gohir.A11G206200' => 'ghi', 'Gohir.D02G085000' => 'ghi', 'Gohir.D05G223600' => 'ghi', 'Gohir.D05G223666' => 'ghi', 'Gohir.D06G032300' => 'ghi', 'Gohir.D07G200700' => 'ghi', 'Gohir.D11G217500' => 'ghi', 'Gorai.001G225300' => 'gra', 'Gorai.007G233500' => 'gra', 'Gorai.009G230700' => 'gra', 'Gorai.009G230800' => 'gra', 'Gorai.010G035600' => 'gra', 'GSVIVG01003598001' => 'vvi', 'GSVIVG01003599001' => 'vvi', 'GSVIVG01003600001' => 'vvi', 'GSVIVG01009147001' => 'vvi', 'GSVIVG01009148001' => 'vvi', 'GSVIVG01012556001' => 'vvi', 'GSVIVG01030144001' => 'vvi', 'HanXRQChr03g0068031' => 'han', 'HanXRQChr08g0232181' => 'han', 'HanXRQChr09g0250891' => 'han', 'HanXRQChr10g0278081' => 'han', 'HanXRQChr10g0306671' => 'han', 'HanXRQChr13g0405081' => 'han', 'HanXRQChr15g0484801' => 'han', 'HanXRQChr15g0484811' => 'han', 'Haze_03064' => 'cav', 'Haze_05749' => 'cav', 'Haze_12565' => 'cav', 'Haze_15056' => 'cav', 'Haze_22336' => 'cav', 'Haze_22337' => 'cav', 'Hma1.2p1_1373F.1_g278700' => 'hma', 'Hma1.2p1_2663F.1_g326410' => 'hma', 'HPP92_002310' => 'vpl', 'HPP92_003827' => 'vpl', 'HPP92_003828' => 'vpl', 'HPP92_013342' => 'vpl', 'HPP92_013349' => 'vpl', 'HPP92_024662' => 'vpl', 'HPP92_024674' => 'vpl', 'Hund08118' => 'sun', 'Hund16541' => 'sun', 'Hund16868' => 'sun', 'Hund27010' => 'sun', 'Lalb_Chr04g0252951' => 'lal', 'Lalb_Chr08g0242431' => 'lal', 'Lalb_Chr11g0065091' => 'lal', 'Lalb_Chr17g0344441' => 'lal', 'Lalb_Chr17g0349321' => 'lal', 'Lj1g0024653' => 'lja', 'Lj2A536G45' => 'lonja', 'Lj4C734G7' => 'lonja', 'Lj4C734T9' => 'lonja', 'Lj8A139G63' => 'lonja', 'LjContig00081g0020061' => 'lja', 'LjContig00408g0016994' => 'lja', 'LjContig00408g0023356' => 'lja', 'Lsat_1_v5_gn_2_125261' => 'lsa', 'Lsat_1_v5_gn_3_61260' => 'lsa', 'Lsat_1_v5_gn_5_121420' => 'lsa', 'Lsat_1_v5_gn_6_104860' => 'lsa', 'Lsat_1_v5_gn_8_28381' => 'lsa', 'Lsat_1_v5_gn_9_74021' => 'lsa', 'Lsat_1_v5_gn_9_74041' => 'lsa', 'Lsat_1_v5_gn_9_76681' => 'lsa', 'Manes.02G146300' => 'mes', 'Manes.02G146400' => 'mes', 'Manes.12G058400' => 'mes', 'Manes.12G127600' => 'mes', 'Manes.18G060600' => 'mes', 'Mapoly0001s0044' => 'mpo', 'Mapoly0057s0092' => 'mpo', 'MBI02_g09037_MAGBIO' => 'mbi', 'MBI06_g36046_MAGBIO' => 'mbi', 'MBI06_g36047_MAGBIO' => 'mbi', 'MBI15_g28685_MAGBIO' => 'mbi', 'MBI15_g43332_MAGBIO' => 'mbi', 'MCO11G474' => 'mco', 'MD01G1037900' => 'mdo', 'MD08G1194100' => 'mdo', 'MD08G1194200' => 'mdo', 'MD09G1134500' => 'mdo', 'MD10G1111400' => 'mdo', 'MD15G1382200' => 'mdo', 'MD15G1382300' => 'mdo', 'MD17G1123400' => 'mdo', 'Medtr1g019825' => 'mtr', 'Medtr4g120350' => 'mtr', 'Medtr5g016640' => 'mtr', 'Medtr5g065880' => 'mtr', 'Medtr5g065900' => 'mtr', 'Medtr5g098710' => 'mtr', 'Medtr6g006810' => 'mtr', 'MELO3C003532.2' => 'cme', 'MELO3C007724.2' => 'cme', 'MELO3C011104.2' => 'cme', 'MELO3C013466.2' => 'cme', 'Migut.H02307' => 'egut', 'Migut.K00779' => 'egut', 'Migut.K01221' => 'egut', 'Migut.M00628' => 'egut', 'Migut.N02863' => 'egut', 'MSTRG.15023' => 'ama', 'MSTRG.22176' => 'ama', 'MSTRG.3743' => 'ama', 'Nitab4.5_0000131g0420' => 'nta', 'Nitab4.5_0000131g0450' => 'nta', 'Nitab4.5_0001468g0030' => 'nta', 'Nitab4.5_0001612g0120' => 'nta', 'Nitab4.5_0003300g0010' => 'nta', 'Nitab4.5_0003300g0020' => 'nta', 'Nitab4.5_0004166g0040' => 'nta', 'Nitab4.5_0010196g0020' => 'nta', 'Nn1g05517' => 'nnu', 'Nn1g07658' => 'nnu', 'Nn5g29925' => 'nnu', 'Oeu016836.1' => 'oeu', 'Oeu022181.1' => 'oeu', 'Oeu030576.1' => 'oeu', 'Oeu033144.1' => 'oeu', 'Oeu055139.1' => 'oeu', 'Os02g0198400' => 'osa', 'Os02g0760200' => 'osa', 'Os08g0478800' => 'osa', 'Os09g0465600' => 'osa', 'Peaxi162Scf00111g00540' => 'pax', 'Peaxi162Scf00281g00319' => 'pax', 'Peaxi162Scf00281g00321' => 'pax', 'Peaxi162Scf00447g00212' => 'pax', 'Peaxi162Scf00447g00213' => 'pax', 'Peaxi162Scf00447g00214' => 'pax', 'Peaxi162Scf58274g00003' => 'pax', 'PGR031G0272' => 'pgr', 'PGR031G0695' => 'pgr', 'PGR042G0314' => 'pgr', 'PGR044G2732' => 'pgr', 'PGSC0003DMG400009848' => 'stu', 'PGSC0003DMG400012910' => 'stu', 'PGSC0003DMG400016206' => 'stu', 'PGSC0003DMG400030128' => 'stu', 'PGSC0003DMG400031098' => 'stu', 'Phvul.008G180200' => 'pvu', 'Phvul.008G180300' => 'pvu', 'Phvul.008G289400' => 'pvu', 'Phvul.009G143550' => 'pvu', 'Potri.002G104000' => 'ptr', 'Potri.002G104100' => 'ptr', 'Potri.004G118950' => 'ptr', 'Potri.014G172000' => 'ptr', 'Pp3c16_3900' => 'ppa', 'Pp3c23_3690' => 'ppa', 'Pp3c24_8030' => 'ppa', 'Pp3c26_8950' => 'ppa', 'Pp3c27_3970' => 'ppa', 'Prupe.1G528400' => 'ppe', 'Prupe.1G528500' => 'ppe', 'Prupe.3G192200' => 'ppe', 'Prupe.6G196800' => 'ppe', 'Psat0s3770g0080' => 'psa', 'Psat0s472g0160' => 'psa', 'Psat2g002000' => 'psa', 'Psat2g066440' => 'psa', 'Psat2g066480' => 'psa', 'Psat7g028200' => 'psa', 'PSO017G3393' => 'pso', 'PSO017G5756' => 'pso', 'PSO170G2511' => 'pso', 'PSO170G6218' => 'pso', 'PSO339G5521' => 'pso', 'PSO541G1871' => 'pso', 'PSO541G3473' => 'pso', 'PSO675G3286' => 'pso', 'PSO675G8881' => 'pso', 'QL04p065705' => 'qlo', 'QL06p047470' => 'qlo', 'QL09p017286' => 'qlo', 'QL09p017299' => 'qlo', 'QL12p018527' => 'qlo', 'RcHm_v2.0_Chr2g0111701' => 'rch', 'RcHm_v2.0_Chr2g0155201' => 'rch', 'RcHm_v2.0_Chr5g0052031' => 'rch', 'RcHm_v2.0_Chr6g0245801' => 'rch', 'RcHm_v2.0_Chr6g0272701' => 'rch', 'RcHm_v2.0_Chr7g0237251' => 'rch', 'RcHm_v2.0_Chr7g0237261' => 'rch', 'RcHm_v2.0_Chr7g0237271' => 'rch', 'RcHm_v2.0_Chr7g0237281' => 'rch', 'RcHm_v2.0_Chr7g0237311' => 'rch', 'RcHm_v2.0_Chr7g0237321' => 'rch', 'Rhsim03G0082700' => 'rsi', 'Rhsim06G0073500' => 'rsi', 'Rhsim06G0073600' => 'rsi', 'Rhsim06G0113600' => 'rsi', 'Rhsim06G0181800' => 'rsi', 'Rhsim06G0182800' => 'rsi', 'Rhsim10G0171900' => 'rsi', 'Sabra02G0081500' => 'sbr', 'Sabra02G0081600' => 'sbr', 'Sabra14G0131500' => 'sbr', 'SalBow2G2226' => 'sbo', 'SalBow3G0955' => 'sbo', 'SalBow3G2528' => 'sbo', 'SalBow3G4013' => 'sbo', 'SalBow3G4159' => 'sbo', 'SalBow5G2081' => 'sbo', 'SalBow5G2722' => 'sbo', 'SalBow8G2763' => 'sbo', 'Sc01g0001070' => 'sci', 'Sc01g0001080' => 'sci', 'Sc15g0007380' => 'sci', 'Sed0003733' => 'sed', 'Sed0007107' => 'sed', 'Sed0007911' => 'sed', 'Sed0013781' => 'sed', 'Sed0014702' => 'sed', 'Sed0016987' => 'sed', 'Sed0020587' => 'sed', 'SEGI_07112' => 'sgi', 'SEGI_19329' => 'sgi', 'SEGI_27560' => 'sgi', 'SEGI_39500' => 'sgi', 'SGA_v2.0_scaffold108G30909' => 'sas', 'SGA_v2.0_scaffold115G32149' => 'sas', 'SGA_v2.0_scaffold28G11891' => 'sas', 'SGA_v2.0_scaffold411G51139' => 'sas', 'SGA_v2.0_scaffold411G51140' => 'sas', 'SGA_v2.0_scaffold48G17819' => 'sas', 'SGA_v2.0_scaffold70G23598' => 'sas', 'SHI06379' => 'shi', 'SHI21964' => 'shi', 'SHI21965' => 'shi', 'SMO115G0127' => 'smo', 'SMO115G0176' => 'smo', 'Solyc04g076090.3' => 'sly', 'Solyc04g076100.4' => 'sly', 'Solyc07g056060.4' => 'sly', 'Solyc11g010490.3' => 'sly', 'Sopen00g007090' => 'spe', 'Sopen04g030070' => 'spe', 'Sopen04g030080' => 'spe', 'Sopen07g029420' => 'spe', 'Sopen11g005270' => 'spe', 'Sp2g18680' => 'spa', 'Sp2g28520' => 'spa', 'Sp6g32990' => 'spa', 'Sp7g22600' => 'spa', 'Sp7g22610' => 'spa', 'TAR381G0262' => 'tar', 'TAR381G0639' => 'tar', 'TAR381G1168' => 'tar', 'TAR381G1629' => 'tar', 'TAR625G0327' => 'tar', 'TAR625G0337' => 'tar', 'TAR629G2855' => 'tar', 'THA.LOC104798734' => 'tha', 'THA.LOC104800044' => 'tha', 'THA.LOC104806836' => 'tha', 'THA.LOC104806846' => 'tha', 'THA.LOC104822527' => 'tha', 'Thecc.01G092200' => 'tca', 'Thecc.01G202300' => 'tca', 'Thecc.08G068600' => 'tca', 'Thecc.08G068700' => 'tca', 'Thhalv10003546m.g' => 'esa', 'Thhalv10003556m.g' => 'esa', 'Thhalv10015247m.g' => 'esa', 'Thhalv10024255m.g' => 'esa', 'Thhalv10024695m.g' => 'esa', 'TPR.G11232' => 'tpr', 'TPR.G16018' => 'tpr', 'TPR.G25727' => 'tpr', 'TPR.G28355' => 'tpr', 'TPR.G35889' => 'tpr', 'TPR.G35896' => 'tpr', 'TPR.G35907' => 'tpr', 'TPR.G40702' => 'tpr', 'TWI12G0831' => 'twi', 'TWI36G0348' => 'twi', 'TWI36G0616' => 'twi', 'TWI36G0898' => 'twi', 'TWI56G0184' => 'twi', 'TWI74G0030' => 'twi', 'unitig_22.g5390' => 'ugi', 'unitig_578.g16183' => 'ugi', 'unitig_62.g23096' => 'ugi', 'unitig_62.g23097' => 'ugi', 'unitig_748.g7041' => 'ugi', 'vmacro12034' => 'vma', 'vmacro12997' => 'vma', 'vmacro21320' => 'vma', 'vmacro21321' => 'vma', 'vmacro21322' => 'vma', 'VMungo0251G0560' => 'vmu', 'VMungo0647G1287' => 'vmu', 'VMungo0647G2095' => 'vmu', 'VMungo0647G2201' => 'vmu', 'VMungo1309G2048' => 'vmu', 'Zm00001eb101090' => 'zma', 'Zm00001eb235970' => 'zma', 'Zm00001eb255590' => 'zma', 'Zm00001eb315420' => 'zma' ) $gf_id = 'HOM05D001083' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001083' ) $data_identifier = 'HOM05D001083' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 12, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 9, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 7, 'sbr' => (int) 3, 'sbo' => (int) 8, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb315420' $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